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Regression Testing C-PAC on SLURM Clusters

(Bridges-2)

This Github repo allows C-PAC developers to run full regression tests on Bridges-2, a cluster under Pittsburgh Computing Center. The scripts in this repo allow you to submit sbatch jobs on Bridges-2.

Note: this repository is currently in the process of transitioning to a CI-initiated flow from a manually initiated flow and contains code and documentation for both during the transition period.

Requirements

For generating an SVG of the interactive correlations graph for a GitHub comment, the system running these scripts needs to have playwright and chromium installed. Once playwright is installed and $PLAYWRIGHT_BROWSERS_PATH is set, chromium can be installed by running

playwright install chromium

Project-specific dependencies

This project is specifically for integration- and regression-testing C-PAC on an HPC using SLURM. Here is a mapping of the interdependencies that are separately maintained and forkable/branchable:

graph TD;
    cpac-slurm-status[<code>cpac-slurm-status</code> CLI] --> childmindresearch/slurm_testing;
    childmindresearch/slurm_testing[childmindresearch/slurm_testing] --> FCP-INDI/C-PAC_regression_dashboard;
    cpac-slurm-status --> image[C-PAC Apptainer image];
    image --> C-PAC[FCP-INDI/C-PAC];
    childmindresearch/slurm_testing --> dashboard;
    FCP-INDI/C-PAC_regression_dashboard[FCP-INDI/C-PAC_regression_dashboard] --> cpac-correlations[<code>cpac-correlations</code> CLI];
    dashboard[fcp-indi.github.io/C-PAC_regression_dashboard] --> gh-pages[FCP-INDI/C-PAC_regression_dashboard@gh-pages];
    gh-pages --> FCP-INDI/C-PAC_regression_dashboard;
    cpac-correlations --> FCP-INDI/CPAC_regtest_pack[FCP-INDI/CPAC_regtest_pack]
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GitHub Actions initiated

Launch a 'lite' regression test run

Set up a GitHub Actions workflow configuration file to call cpac-slurm-status launch. Use contexts, secrets and environment variables to pass the required variables to the script from GitHub Actions.

Required commandline parameters or environment variables

commandline parameter environment variable description required
--comparison-path,
--comparison_path		 $_CPAC_STATUS_COMPARISON_PATH Path to previous run (top level containing the various DATA_SOURCEs) to correlate against. ✅
--dashboard-repo,
--dashboard_repo		 $_CPAC_STATUS_DASHBOARD_REPO FCP-INDI/C-PAC_regression_dashboard or {owner}/{repo} name of drop-in replacement (e.g., a fork of FCP-INDI/C-PAC_regression_dashboard.) ✅
--home-dir $_CPAC_STATUS_HOME_DIR Home directory of the machine user on the remote server (e.g., /ocean/projects/med####p/${USERNAME}). ✅
--image $_CPAC_STATUS_IMAGE The name and tag of the image to test (e.g., ghcr.io/fcp-indi/c-pac:nightly). ✅
--owner $_CPAC_STATUS_OWNER The owner of the C-PAC repository being tested (e.g., FCP-INDI). ✅
--path-extra,
--path_extra		 $_CPAC_STATUS_PATH_EXTRA Any paths that need to be added to PATH to run these scripts on the remote server as the machine user. ✅
--repo $_CPAC_STATUS_REPO The name of the C-PAC repository being tested (e.g., C-PAC). ✅
--sha $_CPAC_STATUS_SHA The SHA of the commit or name of the branch or tag being tested. ✅
--slurm-testing-branch,
--slurm_testing_branch		 $_CPAC_STATUS_SLURM_TESTING_BRANCH Branch of slurm_testing_repo to use for testing ✅
--slurm-testing-repo,
--slurm_testing_repo		 $_CPAC_STATUS_SLURM_TESTING_REPO childmindresearch/slurm_testing or {owner}/{repo} name of drop-in replacement (e.g., a fork of childmindresearch/slurm_testing.) ✅
--token-file,
--token_file		 $_CPAC_STATUS_TOKEN_FILE Path on testing server to a GitHub personal access token with adequate permissions to update GitHub Checks. ✅
--dry-run N/A Simulate rather than run. ❌
N/A $PLAYWRIGHT_BROWSERS_PATH Path to directory containing Playwright Chromium installation. defaults to ${_CPAC_STATUS_HOME_DIR}/.playwright_browsers if not set.

Steps for launch from GitHub Actions

  1. Get branch to test (e.g.).
  2. Configure action to authenticate to remote server (e.g.).
  3. Initiate GitHub Check for test runs as "pending" (e.g).
  4. Launch the test on the remote server. We're currently using the GitHub Actions Marketplace Action SSH Remote Commands by Bo-Yi Wu to facilitate this step (e.g.).
  5. Remove the configuration from step 2 above (e.g.)
Example call to launch script
sbatch \
  cpac_slurm_status launch \
  --wd="${{ env.SSH_WORK_DIR }}/logs/${{ github.sha }}" \
  --comparison-path="${{ env.COMPARISON_PATH }}" \
  --dashboard-repo="${{ env.DASHBOARD_REPO}}" \
  --home-dir="${{ env.SSH_WORK_DIR }}" \
  --image="${{ env.DOCKER_TAG }}" \
  --owner="${{ github.repository_owner }}" \
  --path-extra="${{ env.GH_CLI_BIN_PATH }}" \
  --repo="${{ github.repository }}" \
  --sha="${{ github.sha }}" \
  --slurm-testing-branch="${{ env.SLURM_TESTING_BRANCH }}" \
  --slurm-testing-repo="${{ env.SLURM_TESTING_REPO }}" \
  --token-file="${{ env.TOKEN_FILE }}"

Once launched, the code from this repository will orchestrate the launches (and eventually the correlations and reporting).

See :octocat: FCP-INDI/C-PAC/.github/workflows/regression_test_lite.yml for an example GitHub Actions workflow configuration file that calls this script.

What this repository does once launched

Note: All jobs run through SLURM; this graph only shows which jobs retrieve information from SLURM.

graph TD
SLURM([SLURM]) --> updateRunStatuses;

launch[[<code>sbatch cpac-slurm-status launch</code>]] --> launch_subgraph;

subgraph TotalStatus
   direction LR
   setPaths["set paths (create if not exist) and GitHub token"] --> loadPickle["load status pickle (if exists)"];

   loadPickle --> updateRunStatuses[update run statuses from SLURM];

   updateRunStatuses --> logRunStatuses[log run statuses];

   logRunStatuses --> writeUpdatedPickle[write updated status pickle];
end

subgraph launch_subgraph[launch.launch]
  direction LR
  build_image <--> SLURM;

  build_image{build Apptainer image} --> TotalStatus;

  build_image --success--> regtest_lite.sh

  regtest_lite.sh[<code>sbatch regression_run_scripts/regtest_lite.sh</code>]
--<code>for PIPELINE in ${PRECONFIGS}; do for DATA in ${DATA_SOURCE}; do for SUBJECT_PATH in ''${DATAPATH}''/sub-*; do</code>--> add["<code>cpac-slurm-status add --wd=${OUT} --data_source=${DATA} --preconfig=${PIPELINE} --subject=${SUBJECT}</code>"]

  add --> NamedTemporaryFile[write and run <code>NamedTemporaryFile</code> based on template in <code>templates</code>]
end

TotalStatus --> push_or_check{ };

push_or_check --"initial_state == 'idle'"--> notIdle{"TotalStatus.status != 'idle'"};

notIdle{"TotalStatus.status != 'idle'"} --true--> updateGitHubCheck[update GitHub check];

push_or_check --"TotalStatus.status != 'pending'"--> uGHC2[update GitHub check];

uGHC2 --> cleanUp["TotalStatus.clean_up()"];

cleanUp --> correlate;

push_or_check --"else"--> check_again_later[check status again in 30 minutes];

check_again_later --> TotalStatus;

subgraph correlate
  direction LR
  setCorrelationDir[set correlations directory] --<code>for data_source in TotalStatus.datasources:\n\tfor preconfig in TotalStatus.preconfigs:</code>--> cpac_yaml[create correlation config YAML];

  cpac_yaml --> cpac_correlations[run <code>cpac_correlations</code> to create JSON file];
end

correlate --> init_branch["commit correlation images to SHA-specific branch in <code>regtest-runlogs<code> repository"];

init_branch --> comment["push comment to commit on GitHub"];
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Manually initiated

Installation Guide

  1. SSH into Bridges-2

  2. In your project home directory (typically /ocean/projects/med####p/{username}), clone this repo

    git clone [email protected]:amygutierrez/slurm_testing.git

  3. You're ready to start testing! 🧑‍💻

What does a C-PAC Regression Test entail?

Regression testing for C-PAC means that certain pipelines and certain datasets will be used for testing. Full regression testing requires ALOT of computaional resources, so will need to run this on a cluster.

Regression testing pipelines tested:

  • default

Regression testing datasets used:

  • HNU_1 (5 subjects)
  • Site-CBIC (4 subjects)
  • Site-SI (3 subjects)

Script Details

This script will run the Apptainer image provided against the pipelines and datasets detailed above. Every pipeline has fixed the random_seed value to 77742777